Hi,
I am still trying to debug the issue with MMPBSA.MPI. I could run the same input files through MMPBSA successfully but always failed with parallel version MMPBSA.MPI.
Now, I have ruled out the previous suspicion that IOError was causing the crash of calculation. The real reason is that a segmentation fault exception was thrown during "calculating ligand contribution..." for GB calculation. To be more specific: "mmpbsa_py_energy -O -i _MMPBSA_gb.mdin -o _MMPBSA_ligand_gb.mdout.0 -p g1dimer_4hexa_nosolv.top -c _MMPBSA_dummyligand.inpcrd.1 -y _MMPBSA_ligand.mdcrd.0 -r _MMPBSA_.restrt_ligand.0 -pdb _MMPBSA_ligand.pdb" gives segmentation fault. There is only 1 frame in _MMPBSA_ligand_gb.mdout.0. The same thing happens to the other 3 processes.
Another odd thing I've noticed was that "50 frames were read in and processed by ptraj for use in calculation" was always showing up at beginning of calculation for both parallel and serial run.
For parallel run:
I checked
_MMPBSA_complex_gb.mdout.0 & _MMPBSA_receptor_gb.mdout.0 13 frames processed
_MMPBSA_complex_gb.mdout.1 & _MMPBSA_receptor_gb.mdout.1 13 frames processed
_MMPBSA_complex_gb.mdout.2 & _MMPBSA_receptor_gb.mdout.2 12 frames processed
_MMPBSA_complex_gb.mdout.3 & _MMPBSA_receptor_gb.mdout.3 12 frames processed
13+13+12+12=50 and it's fine
_MMPBSA_ligand_gb.mdout.0 1 frame processed then crashed
_MMPBSA_ligand_gb.mdout.1 1 frame processed then crashed
_MMPBSA_ligand_gb.mdout.2 0 frame processed then crashed
_MMPBSA_ligand_gb.mdout.3 1 frame processed then crashed
For serial run:
I checked
_MMPBSA_complex_gb.mdout 50 frames processed
_MMPBSA_receptor_gb.mdout 62 frames processed
_MMPBSA_ligand_gb.mdout 100 frames processed
Could anyone give me some explanation?
Thanks
Ye
On Jul 6, 2011, at 9:51 AM, Ye Fan wrote:
> Hi Bill,
>
> Yes, I've downloaded the bugfix.all at "http://ambermd.org/bugfixesat.html" for version 1.5 and patched the source codes before compiling them. If you could tell me which bug particularly you are looking for, I can manually check it again.
>
> Thanks
> Ye
>
> On Jul 5, 2011, at 5:14 PM, Bill Miller III wrote:
>
>> Have you applied all the AmberTools 1.5 bugfixes? This was a bug that I
>> found in the code a while back, and I thought it had been added to the known
>> patches.
>>
>> -Bill
>>
>> On Tue, Jul 5, 2011 at 3:53 PM, Ye Fan <yefan.ncsa.uiuc.edu> wrote:
>>
>>> Hi Bill,
>>>
>>> This is the last part of _MMPBSA_receptor_pb.mdout file:
>>>
>>>
>>> --------------------------------------------------------------------------------
>>> 4. RESULTS
>>>
>>> --------------------------------------------------------------------------------
>>>
>>> POST-PROCESSING OF TRAJECTORY ENERGIES
>>> trajectory generated by ptraj
>>> minimizing coord set # 1
>>> Total surface charge 1.9723
>>> Reaction field energy -3570.1196
>>> Cavity solvation energy 54.6777
>>>
>>>
>>> Maximum number of minimization cycles reached.
>>>
>>>
>>> FINAL RESULTS
>>>
>>>
>>>
>>> NSTEP ENERGY RMS GMAX NAME NUMBER
>>> 1 -3.1384E+03 1.7292E+01 1.0289E+02 N 680
>>>
>>> BOND = 329.2644 ANGLE = 939.0290 DIHED =
>>> 1182.0229
>>> VDWAALS = -670.5602 EEL = -7995.5664 EPB =
>>> -3570.1813
>>> 1-4 VDW = 394.1857 1-4 EEL = 6198.7732 RESTRAINT =
>>> 0.0000
>>> ECAVITY = 54.6777 EDISPER = 0.0000
>>> minimization completed, ENE= -.31383551E+04 RMS= 0.172922E+02
>>> minimizing coord set # 2
>>> 67.611999999999995 5.7789999999999999 0.63300000000000001
>>> pb_fdfrc(): Atom out of focusing box 251 59 44
>>>
>>> ------------------------------------------------------------------------------------------------------------------------
>>>
>>> I hope it helps.
>>>
>>> Thanks
>>> Ye
>>>
>>> On Jul 5, 2011, at 11:57 AM, Bill Miller III wrote:
>>>
>>>> What is at the end of the _MMPBSA_receptor_pb.mdout file? There should be
>>> an
>>>> error message or warning in that file that should help explain the error
>>>> based on where the calculation ended.
>>>>
>>>> -Bill
>>>>
>>>> On Tue, Jul 5, 2011 at 12:50 PM, Ye Fan <yefan.ncsa.uiuc.edu> wrote:
>>>>
>>>>> Hi Jason,
>>>>>
>>>>> I have added the "use_sander=1" in the $general section of input file.
>>>>> However, the computation failed with sander error:
>>>>>
>>>>>
>>>>>
>>> ================================================================================
>>>>> Reading command-line arguments and input files...
>>>>> Loading and checking parameter files for compatibility...
>>>>> ptraj found! Using /u/ncsa/yefan/apps/amber11-gnu/bin/ptraj
>>>>> sander found! Using /u/ncsa/yefan/apps/amber11-gnu/bin/sander for GB
>>>>> calculations
>>>>> sander found! Using /u/ncsa/yefan/apps/amber11-gnu/bin/sander for PB
>>>>> calculations
>>>>> Preparing trajectories for simulation...
>>>>> 50 frames were read in and processed by ptraj for use in calculation.
>>>>>
>>>>> Beginning GB calculations with sander...
>>>>> calculating complex contribution...
>>>>> calculating receptor contribution...
>>>>> calculating ligand contribution...
>>>>>
>>>>> Beginning PB calculations with sander...
>>>>> calculating complex contribution...
>>>>> calculating receptor contribution...
>>>>> Error: sander error during PB calculations!
>>>>> NOTE: All files have been retained for debugging purposes. Type
>>> MMPBSA.py
>>>>> --clean to erase these files.
>>>>>
>>>>>
>>> ================================================================================
>>>>>
>>>>> I have serial sander built with gnu compiler.
>>>>>
>>>>> So, I went into the test folder of Amber11 and did `make test.serial.MM
>>> `.
>>>>> It failed at (I wanted to test sander built):
>>>>> ========================================
>>>>> CALCULATING TEST: 02_MMPBSA_Stability
>>>>> ./Run.mmpbsa.test: Program error
>>>>> make: *** [test.mm_pbsa] Error 1
>>>>> ========================================
>>>>>
>>>>> I also did test under $AMBERHOME/AmberTools/test/mmpbsa_py.
>>>>>
>>>>> It failed at:
>>>>> ===========================
>>>>> cd 06_NAB_Nmode && ./Run.nmode
>>>>> diffing FINAL_RESULTS_MMPBSA.dat.save with FINAL_RESULTS_MMPBSA.dat
>>>>> possible FAILURE: check FINAL_RESULTS_MMPBSA.dat.dif
>>>>> ...
>>>>> ...
>>>>> cd 08_Stability && ./Run.stability
>>>>> ./Run.stability: Program error
>>>>> make: *** [STABILITY] Error 1
>>>>> ===========================
>>>>>
>>>>> Any idea what's going wrong?
>>>>>
>>>>> Thank you very much
>>>>> Ye
>>>>>
>>>>>
>>>>> On Jul 2, 2011, at 7:18 PM, Jason Swails wrote:
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> If you have Amber11 available, try setting the variable "use_sander=1"
>>> in
>>>>>> your MMPBSA input file (in the &general section). I'm not sure what's
>>>>>> happening here, but your filesystem seems to be choking on simultaneous
>>>>> file
>>>>>> accesses or something like that (perhaps the way NAB handles files is
>>>>>> causing some grief, maybe you'll have better luck with sander, although
>>>>> it
>>>>>> will take longer).
>>>>>>
>>>>>> HTH,
>>>>>> Jason
>>>>>>
>>>>>> On Fri, Jul 1, 2011 at 5:08 PM, Ye Fan <yefan.ncsa.uiuc.edu> wrote:
>>>>>>
>>>>>>> Hi Jason,
>>>>>>>
>>>>>>> The serial version is only having some minor issues.
>>>>>>>
>>>>>>> Following is the output:
>>>>>>>
>>>>>>>
>>>>>
>>> ----------------------------------------------------------------------------------------------------------------------------------------------------------------
>>>>>>> Reading command-line arguments and input files...
>>>>>>> Loading and checking parameter files for compatibility...
>>>>>>> ptraj found! Using /u/ncsa/yefan/apps/amber11-gnu/bin/ptraj
>>>>>>> mmpbsa_py_energy found! Using
>>>>>>> /u/ncsa/yefan/apps/amber11-gnu/bin/mmpbsa_py_energy for GB
>>> calculations
>>>>>>> mmpbsa_py_energy found! Using
>>>>>>> /u/ncsa/yefan/apps/amber11-gnu/bin/mmpbsa_py_energy for PB
>>> calculations
>>>>>>> Preparing trajectories for simulation...
>>>>>>> 50 frames were read in and processed by ptraj for use in calculation.
>>>>>>>
>>>>>>> Beginning GB calculations with mmpbsa_py_energy...
>>>>>>> calculating complex contribution...
>>>>>>> calculating receptor contribution...
>>>>>>> calculating ligand contribution...
>>>>>>>
>>>>>>> Beginning PB calculations with mmpbsa_py_energy...
>>>>>>> calculating complex contribution...
>>>>>>> PB Info in pb_read(): npopt has been overwritten with inp
>>>>>>> Total surface charge 2.9598
>>>>>>> Reaction field energy -4821.5307
>>>>>>> Cavity solvation energy 77.1504
>>>>>>> ...
>>>>>>> ...
>>>>>>> Reaction field energy -4763.0697
>>>>>>> Cavity solvation energy 78.8077
>>>>>>> calculating receptor contribution...
>>>>>>> PB Info in pb_read(): npopt has been overwritten with inp
>>>>>>> Total surface charge 1.9721
>>>>>>> Reaction field energy -3552.3284
>>>>>>> ...
>>>>>>> ...
>>>>>>> Reaction field energy -5066.6010
>>>>>>> Cavity solvation energy 62.5406
>>>>>>> calculating ligand contribution...
>>>>>>> PB Info in pb_read(): npopt has been overwritten with inp
>>>>>>> Total surface charge 0.9867
>>>>>>> Reaction field energy -2684.2835
>>>>>>> ...
>>>>>>> ...
>>>>>>> Reaction field energy -2737.6791
>>>>>>> Cavity solvation energy 34.1780
>>>>>>>
>>>>>>> Timing:
>>>>>>> Total setup time: 0.031 min.
>>>>>>> Creating trajectories with Ptraj: 0.084 min.
>>>>>>> Total calculation time: 29.421 min.
>>>>>>> Total GB calculation time (sander): 1.623 min.
>>>>>>> Total PB calculation time (sander): 27.798 min.
>>>>>>> Statistics calculation & output writing: 0.002 min.
>>>>>>> Total time taken: 29.538 min.
>>>>>>>
>>>>>>>
>>>>>>> MMPBSA.py Finished! Thank you for using. Please report any bugs to
>>>>>>> amber.ambermd.org
>>>>>>>
>>>>>>>
>>>>>
>>> ----------------------------------------------------------------------------------------------------------------------------------------------------------------
>>>>>>>
>>>>>>> Thanks
>>>>>>> Ye
>>>>>>>
>>>>>>> On Jul 1, 2011, at 11:39 AM, Jason Swails wrote:
>>>>>>>
>>>>>>>> Does it work in serial if you test it on just the first couple
>>> frames?
>>>>>>>>
>>>>>>>> On Fri, Jul 1, 2011 at 10:00 AM, Ye Fan <yefan.ncsa.uiuc.edu> wrote:
>>>>>>>>
>>>>>>>>> Hi,
>>>>>>>>>
>>>>>>>>> I came across some errors when running MMPBSA.MPI. Following is the
>>>>>>> output:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>
>>> ---------------------------------------------------------------------------------------------------------------------------------------------------------------------
>>>>>>>>> Running MMPBSA.MPI on 4 processors...
>>>>>>>>> Reading command-line arguments and input files...
>>>>>>>>> Loading and checking parameter files for compatibility...
>>>>>>>>> ptraj found! Using /u/ncsa/yefan/apps/amber11-gnu/bin/ptraj
>>>>>>>>> mmpbsa_py_energy found! Using
>>>>>>>>> /u/ncsa/yefan/apps/amber11-gnu/bin/mmpbsa_py_energy for GB
>>>>> calculations
>>>>>>>>> mmpbsa_py_energy found! Using
>>>>>>>>> /u/ncsa/yefan/apps/amber11-gnu/bin/mmpbsa_py_energy for PB
>>>>> calculations
>>>>>>>>> Preparing trajectories for simulation...
>>>>>>>>> 2150 frames were read in and processed by ptraj for use in
>>>>> calculation.
>>>>>>>>>
>>>>>>>>> Beginning GB calculations with mmpbsa_py_energy...
>>>>>>>>> calculating complex contribution...
>>>>>>>>> calculating receptor contribution...
>>>>>>>>> calculating ligand contribution...
>>>>>>>>> close failed in file object destructor:
>>>>>>>>> IOError: [Errno 9] Bad file descriptor
>>>>>>>>> close failed in file object destructor:
>>>>>>>>> IOError: [Errno 9] Bad file descriptor
>>>>>>>>> close failed in file object destructor:
>>>>>>>>> IOError: [Errno 9] Bad file descriptor
>>>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>
>>> ---------------------------------------------------------------------------------------------------------------------------------------------------------------------
>>>>>>>>>
>>>>>>>>> I have AmberTool 1.5 with Amber 11 fully patched and compiled with
>>> gnu
>>>>>>>>> compiler. Mpi4py is built with openmpi-1.4.3.
>>>>>>>>>
>>>>>>>>> Any idea what's going wrong?
>>>>>>>>>
>>>>>>>>> Thanks
>>>>>>>>> Ye
>>>>>>>>> _______________________________________________
>>>>>>>>> AMBER mailing list
>>>>>>>>> AMBER.ambermd.org
>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> Jason M. Swails
>>>>>>>> Quantum Theory Project,
>>>>>>>> University of Florida
>>>>>>>> Ph.D. Candidate
>>>>>>>> 352-392-4032
>>>>>>>> _______________________________________________
>>>>>>>> AMBER mailing list
>>>>>>>> AMBER.ambermd.org
>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> AMBER mailing list
>>>>>>> AMBER.ambermd.org
>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Jason M. Swails
>>>>>> Quantum Theory Project,
>>>>>> University of Florida
>>>>>> Ph.D. Candidate
>>>>>> 352-392-4032
>>>>>> _______________________________________________
>>>>>> AMBER mailing list
>>>>>> AMBER.ambermd.org
>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Bill Miller III
>>>> Quantum Theory Project,
>>>> University of Florida
>>>> Ph.D. Graduate Student
>>>> 352-392-6715
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>>
>> --
>> Bill Miller III
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Graduate Student
>> 352-392-6715
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
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Received on Fri Jul 15 2011 - 10:00:03 PDT
